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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from inducible ES stable cell lines

ABSTRACT: In order to identify the effects of the induction of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the different inducible cell lines Transcriptome analysis of the inducible transgenic mouse ES cell lines For the analysis on the different inducible cell lines, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 17 and 24 hours; RNA extracted from un-induced clones was used as control. Total RNA extracted from parental cell line EBRTcH3 (EB3) was used as additional control.

ORGANISM(S): Mus musculus

SUBMITTER: Rossella De Cegli

PROVIDER: E-GEOD-32015 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation.

De Cegli Rossella R Iacobacci Simona S Flore Gemma G Gambardella Gennaro G Mao Lei L Cutillo Luisa L Lauria Mario M Klose Joachim J Illingworth Elizabeth E Banfi Sandro S di Bernardo Diego D

Nucleic acids research 20121123 2

Gene expression profiles can be used to infer previously unknown transcriptional regulatory interaction among thousands of genes, via systems biology 'reverse engineering' approaches. We 'reverse engineered' an embryonic stem (ES)-specific transcriptional network from 171 gene expression profiles, measured in ES cells, to identify master regulators of gene expression ('hubs'). We discovered that E130012A19Rik (E13), highly expressed in mouse ES cells as compared with differentiated cells, was a ...[more]

PMID: 23180766

Similar Datasets

Expression data from inducible ES stable cell line

Project description:In order to identify the effects of the induction of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line. Transcriptome analysis of the inducible transgenic mouse ES cell line. The E13 inducible cell lines derived from parental EB3 cell line. The cell line EB3 was obtained from the laboratory of Dr Hitoshi Niwa as previously described in (Masui S et al., 2005). Tthe specific mouse gene is E130012A19Rik. For the analysis on the inducible not-tagged cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 48 hours; RNA extracted from un-induced clones was used as control.

2012-12-13 | E-GEOD-31166 | biostudies-arrayexpress

E130012A19Rik: Biomarker of Pluripotent Stem Cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-12-13 | E-GEOD-31701 | biostudies-arrayexpress

Over-expression of FGFR2b from a tetracycline-inducible expression vector

Project description:Genome-wide association studies for breast cancer have identified over 80 different risk regions in the genome, with the FGFR2 locus consistently identified as the most strongly associated locus. However, we know little about the mechanisms by which the FGFR2 locus mediates risk or the pathways in which multiple risk loci may combine to cause disease. Here we use a systems biology approach to elucidate the regulatory networks operating in breast cancer and examine the role of FGFR2 in mediating risk. Using model systems we identify FGFR2-regulated genes and, combining variant set enrichment and eQTL analysis, show that these are preferentially linked to breast cancer risk loci. Our results support the concept that cancer-risk associated genes cluster in pathways The data consists of 125 microarray samples from MCF-7 cells treated under different conditions, at 5 time points (0, 3, 6, 12 and 24 h) in order to perturb FGFR2 signalling by overexpressing the full length FGFR2b from a tetracycline-inducible expression vector. The data have been pre-processed in R using the beadarray package, and are presented in the form of log2 expression values. The experiment was carried out on 11 Humanv4 BeadChips using 12 samples per BeadChip. The original arrays contains 48324 features, with a mean of 22 beads per feature (Standard Deviation of 5)

2013-07-17 | E-GEOD-48927 | biostudies-arrayexpress

A mouse Embryonic Stem Cell Bank for inducible overexpression of human chromosome 21 genes

Project description:The HSA21-mES Cell Bank includes, in triplicate clones, thirty-two murine orthologs of HSA21 genes, which can be overexpressed in an inducible manner using the Tet-off system integrated in the Rosa26 locus. The following subset of twenty clones were characterized by microarray analysis: Bach1, Erg, Ets2, Gabpa, ZFP295, Nrip1, Olig1, Olig2, Pknox1, 1810007M14Rik, Runx1, Aire, Sim2, Dscr1, DYRK1A, SNF1LK, Ripk4 , Hunk, Pdxk, Pfkl. Each triplicate clone was transcriptionally profiled by microarray analysis using Affymetrix Mouse 430_2 arrays before and after induction (Affymetrix 430A_2 in case of Runx1), yielding six arrays for each overexpression experiment.

2010-12-06 | E-GEOD-19836 | biostudies-arrayexpress

Signaling from the secretory granule to the nucleus: Uhmk1 and PAM

Project description:Neurons and endocrine cells package peptides in secretory granules (large dense core vesicles; LDCVs) for storage and stimulated release. Studies of PAM, an essential secretory granule membrane enzyme, revealed a pathway that can relay information from secretory granules to the nucleus, resulting in alterations in gene expression. The cytosolic domain of PAM, a type 1 membrane enzyme essential for the production of amidated peptides, is basally phosphorylated by Uhmk1 and other Ser/Thr kinases. Proopiomelanocortin processing in AtT-20 corticotrope tumor cells was increased when Uhmk1 expression was reduced. Uhmk1 was concentrated in the nucleus, but cycled rapidly between nucleus and cytosol. Endoproteolytic cleavage of PAM releases a soluble cytosolic domain (CD) fragment that localizes to the nucleus. Localization of PAM-CD to the nucleus was decreased when PAM-CD with phosphomimetic mutations was examined and when active Uhmk1 was simultaneously over-expressed. Membrane-tethering Uhmk1 did not eliminate its ability to exclude PAM-CD from the nucleus, suggesting that cytosolic Uhmk1 could cause this response. Microarray analysis demonstrated the ability of PAM to increase expression of a small subset of genes, including aquaporin 1 (Aqp1) in AtT-20 cells. Aqp1 mRNA levels were higher in wildtype mice than in mice heterozygous for PAM, indicating that a similar relationship occurs in vivo. Expression of PAM-CD also increased Aqp1 levels while expression of Uhmk1 diminished Aqp1 expression. The outlines of a pathway that ties secretory granule metabolism to the transcriptome are thus apparent. Three separate clones of AtT-20 mouse corticotrope tumor cells stably transfected with doxycycline-inducible rat PAM-1 (clones 14, 6_1, 6_2) were treated with cotrol or doxycycline medium for 48 hours. Total mRNA was isolated and hybridized to an Illumina MouseWG-6 v 2.0 whole genome BeadChip.

2010-07-29 | E-GEOD-22509 | biostudies-arrayexpress

Inactivation of CDK2 is synthetic lethal to MYCN-overexpressing cancer cells

Project description:Two genes have a synthetic lethal relationship when silencing or inhibition of one gene is only lethal in the context of a mutation or activation of the second gene. This situation offers an attractive therapeutic strategy, as inhibition of such a gene will only trigger cell death in tumor cells with an activated second oncogene but spare normal cells without activation of the second oncogene. Here we present evidence that CDK2 is synthetic lethal to neuroblastoma cells with MYCN amplification and overexpression. Neuroblastomas are childhood tumors with an often lethal outcome. Twenty percent of the tumors have MYCN amplification and these tumors are ultimately refractory to any therapy. Targeted silencing of CDK2 by three RNA interference techniques induced apoptosis in MYCN-amplified neuroblastoma cell lines, but not in MYCN single copy cells. Silencing of MYCN abrogated this apoptotic response in MYCN-amplified cells. Inversely, silencing of CDK2 in MYCN single copy cells did not trigger apoptosis, unless a MYCN transgene was activated. The MYCN induced apoptosis after CDK2 silencing was accompanied by nuclear stabilization of P53 and mRNA profiling showed up-regulation of P53 target genes. Silencing of P53 rescued the cells from MYCN-driven apoptosis. The synthetic lethality of CDK2 silencing in MYCN activated neuroblastoma cells can also be triggered by inhibition of CDK2 with a small molecule drug. Treatment of neuroblastoma cells with Roscovitine, a CDK inhibitor, at clinically achievable concentrations induced MYCN-dependent apoptosis. The synthetic lethal relation between CDK2 and MYCN indicates CDK2 inhibitors as potential MYCN-selective cancer therapeutics. CDK2 shRNA in a tet repressor system was stably transfected in the IMR32 cell line. Time course analysis was performed in triplicate after induction of CDK2 shRNA at 5 time points.

2014-05-19 | E-GEOD-16480 | biostudies-arrayexpress

Transcription profiling of mouse hematopoietic Baf-3 cells inducibly expressing transcription factor Sp1

Project description:Inducible expression of transcription factor Sp1 in hematopoietic baf-3 cells

2009-02-10 | E-MEXP-1702 | biostudies-arrayexpress

RNA-seq of human SH-EP neuroblastoma cell line with SOX11 overexpression as compared to control at 9h timepoint

Project description:RNA-seq to define downstream targets of adrenergic SOX11 upon 1ug/ml doxycyline inducible SOX11 overexpression in a SOX11 non-expressing mesenchymal cell line SH-EP. Analysis was performed 48h upon treatment with doxycycline, control samples are the untreated cells. 2 biological replicates were used.

2022-12-13 | E-MTAB-11892 | biostudies-arrayexpress

RNA-seq of human SH-EP neuroblastoma cell line with SOX11 overexpression as compared to control

2022-12-13 | E-MTAB-9338 | biostudies-arrayexpress

Gene expression profiling of the effect of elevated TRIB3 expression on the transcriptional response to glucose deprivation

Project description:Gene expression profiling of HEK293-derived cell lines that are stably transfected with either a tetracycline-inducible TRIB3 expression construct (TRIB3-293 cells), tetracycline-inducible ATF4 expression construct (ATF4-293 cells) or the corresponding empty vector (Vector-293 cells). Samples from tetracycline-treated and tetracycline-untreated cell cultures were collected after a 24-hour (TRIB3-293 cells, Vector-293) or 4-hour (ATF4-293) incubation in growth medium either with or without glucose.

2016-02-09 | E-MTAB-3318 | biostudies-arrayexpress

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